- Supplemental Data from: Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH (2014) Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proceedings of the National Academy of Sciences 111 (44) E4736–E4742. doi: 10.1073/pnas.1416574111

- Raw data available through NCBI SRA BioProject PRJNA257113

## File descriptions

##### 70cephsp.phytab
Nucleotide alignments of the 13 loci used to construct cephalopod phylogeny. (Tab-delimited Phytab format: species/locus/identifier/sequence.)

##### 70spNT.phy.tre
ML tree inferred with RAxML under GTRGAMMA across 13 loci. Bootstrap support from 1000 iteration provided as node labels. (Newick format)

##### BLchar70sp.csv
Character states for presence/absence of bacteriogenic bioluminescent organs. 

##### alllibs90.blastn.counts.csv
Illumina reads from each library were mapped to the organism's collective Trinity-assembled transcriptome. All transcriptomes from each species were pooled and clustered to 90% similarity. Orthologous transcripts between species were estimated by best reciprocal BLAST match. Counts were aggregated from original transcripts belonging to each ortholog.

##### alllibs90.blastn.uniprotID.counts.csv
Illumina reads from each library were mapped to the organism's collective Trinity-assembled transcriptome using RSEM. All transcriptomes from each species were pooled and clustered to 90% similarity. Orthologous transcripts between species and the UniProt90 reference database were estimated by best reciprocal BLAST match. Counts were aggregated from original transcripts belonging to each UniProt match.

##### es90_orfs.tar
Euprymna scolopes transcriptomes, clustered to 90% similarity prior to ORF prediction by Trinity. (Compressed, fasta format)

##### ue90_orfs.tar
Uroteuthis edulis transcriptomes, clustered to 90% similarity prior to ORF prediction by Trinity. (Compressed, fasta format)

##### Ue90fastas.tar
Uroteuthis edulis transcriptomes (Trinity-assembled from 6 RNAseq tissues) pooled for 3 individuals, clustered to 90% similarity with CD-HIT-EST. (Compressed, fasta format)

##### Es90fastas.tar
Euprymna scolopes transcriptomes (Trinity-assembled from 6 RNAseq tissues) pooled for 3 individuals, clustered to 90% similarity with CD-HIT-EST. (Compressed, fasta format)